Project Summary: Genetic variants that alter gene expression comprise a substantial component of the genetic basis of many organismal traits and diseases. However, a heavy reliance on mRNA levels as a measure of gene expression has left us with only a rudimentary knowledge of how genetic variation influences protein abundance. In particular, genetic effects on protein degradation have not been comprehensively characterized in any species. This is a critical limitation because protein degradation is the primary post- transcriptional regulator of protein abundance and impaired protein degradation is implicated in a variety of devastating diseases, including neurodegenerative diseases, cancers, and immune disorders. Genetic effects on protein degradation may, therefore, constitute a critical missing link between individual genetic variation and the poorly understood complex genetic basis of these diseases. The overarching goal of this proposal is to address these limitations by systematically and comprehensively mapping genetic influences on protein degradation in the budding yeast Saccharomyces cerevisiae. I will leverage the many advantages of the yeast model system for complex trait genetics to map genetic influences on the ubiquitin-proteasome system (UPS), the cell?s primary protein degradation pathway, and the degradation of a set of individual proteins. I propose two experimental aims to accomplish this goal. For the first, I will perform quantitative trait locus (QTL) mapping of genetic influences on UPS activity. To do so, I will develop a series of novel fluorescent reporters that measure the activity of ubiquitin-dependent and ubiquitin-independent UPS protein degradation. These reporters will be used for bulk segregant QTL mapping in a cross of two genetically divergent yeast strains. This QTL mapping method has exceptionally high statistical power to detect variant effects and is thus an ideal approach for initially characterizing genetic influences on UPS activity. In the second aim, I will use the same QTL mapping method to characterize genetic influences on the degradation of a set of individual yeast proteins using tandem fluorescent timers (TFTs), constructs that measure individual protein degradation rate. The proteins selected for this aim comprise diversity in protein half-life, coding sequence variation between strains, function, subcellular localization, and gene essentiality in yeast. This diversity of features maximizes the potential to capture variation in a wide array of genetic regulatory mechanisms impacting protein degradation. Fine-mapping of QTL from Aims 1 and 2 to the level of causal genes and nucleotides will help clarify molecular mechanisms of variant effects. Collectively, these aims will (1) provide the first systematic dissection of the genetic architecture of protein degradation, (2) identify molecular mechanisms of variant effects on protein degradation, and (3) develop novel tools for the study of protein degradation. My results will lay the groundwork for future efforts to understand how genetic effects on protein degradation contribute to the complex genetic basis of the many diseases marked by impairments in this process.